FlowQuant User Manual - University of Ottawa Heart Institute

FlowQuant User Manual - University of Ottawa Heart Institute
FlowQuant©
User Manual
Software Version 2.2.4
January 2014
University of Ottawa Heart Institute
Cardiac PET Centre
40 Ruskin St.
Ottawa, Ontario
K1Y 4W7
Canada
(613)-761-4275
www.ottawaheart.ca
[email protected]
FlowQuant©
User Manual
Disclaimer
FlowQuant© is protected under international copyright law. Use of this software without the sole
permission of the University of Ottawa Heart Institute, Cardiac PET Centre is illegal.
FlowQuant© is a research tool that is still in the development phase and is not approved for clinical
use. Any use of FlowQuant© is under the responsibility of the user and the results are not
guaranteed by the developer.
ExcelTM is a registered trademark of Microsoft Corporation.
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Table of Contents
Disclaimer ...............................................................................................................................................1
Table of Contents....................................................................................................................................2
Introduction ............................................................................................................................................5
Minimum System Requirements ............................................................................................................6
Terminology and Acronyms ....................................................................................................................7
FlowQuant© Graphical User Interface ...................................................................................................8
Menu ..................................................................................................................................................9
Toolbar ............................................................................................................................................ 10
Study List ......................................................................................................................................... 11
Comments ....................................................................................................................................... 11
Buttons ............................................................................................................................................ 11
Routine Use ......................................................................................................................................... 13
Creating a Study .............................................................................................................................. 13
Adding an Analysis Entry ................................................................................................................. 14
Adding a Scan Entry ......................................................................................................................... 15
Processing a Study ........................................................................................................................... 18
Reorientation .............................................................................................................................. 18
LV Modeling (Sampling) .............................................................................................................. 19
Dynamic Polar-Map .................................................................................................................... 23
Blood ROI Processing .................................................................................................................. 24
Kinetic Modeling ......................................................................................................................... 24
Single Window Processing (* in Beta testing) ............................................................................. 26
Analysis ....................................................................................................................................... 27
Results ............................................................................................................................................. 33
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Dynamic Splash Display (DSD) ......................................................................................................... 33
Additional Features ............................................................................................................................. 36
Removing an Entry .......................................................................................................................... 37
Duplicating an Entry ........................................................................................................................ 38
Multiple Entry Selection .................................................................................................................. 38
Viewing Data ................................................................................................................................... 38
Analysis Settings .................................................................................................................................. 41
Settings Hierarchy ........................................................................................................................... 41
Entry Settings .................................................................................................................................. 42
Study Settings .................................................................................................................................. 46
General Options .......................................................................................................................... 46
Color Options .............................................................................................................................. 48
Default Analysis Options ............................................................................................................. 49
Rest-Stress Flow Analysis Options .............................................................................................. 49
Making Current Study Settings the Default Settings .................................................................. 50
Reverting to the Default Study Settings...................................................................................... 50
Exporting the Study Settings ....................................................................................................... 50
Importing Study Settings from another File ............................................................................... 50
Tools..................................................................................................................................................... 52
Close All Figures............................................................................................................................... 52
Clean Study Directory ...................................................................................................................... 52
Update Scan Files Directories .......................................................................................................... 52
Image Cropping Tool ....................................................................................................................... 53
Motion Correction Tool ................................................................................................................... 56
Administrator Tools ......................................................................................................................... 58
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Data – Export Dynamic Data ........................................................................................................... 59
Data – Export KM Results ................................................................................................................ 59
Data – Export ROI Coordinates........................................................................................................ 60
Special Considerations for Small Animal PET Image Processing ......................................................... 61
Additional Documentation .................................................................................................................. 63
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Introduction
FlowQuant© is developed by the University of Ottawa Heart Institute, Cardiac PET Centre.
Originally, FlowQuant© was intended as a tool for quantification of physiological function from
dynamic positron emission tomography (PET). However, additional tools and analyses are
continuously being added to support static and gated imaging of nuclear imaging modalities.
FlowQuant© is a menu based GUI which is able to process large sets of scans, both in a research
and clinical setting. Typical processing of dynamic images includes the following steps:
1. Scan processing:
a. Generating polar-maps (uptake and dynamic sequence) and sampling the LV blood
pool time-activity-curve (TAC).
b. Kinetic modeling using the dynamic polar-map and blood TAC.
2. Analysis of the results of sets of scans. This includes mismatch analysis and rest/stress
comparison.
This document provides information on using the FlowQuant© tool and its features. More specific
information about sampling polar-maps, kinetic models, and analysis tools is published in literature.
The goal of this document is to form a user manual, not to describe the science. It is therefore
expected that the reader has sufficient background in nuclear-cardiac imaging and be current with
the field of quantitative imaging.
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Minimum System Requirements
Before attempting to run FlowQuant©, please ensure that your system meets the minimum
requirements listed below. In the event that your system does not meet these specifications, the
proper functioning of the program is not guaranteed by the developer.
Minimum requirements:
Pentium D
4 GB of RAM
10 GB of hard drive space available
1280 x 800 screen resolution
32 bit colour
Windows XP or Vista operating system
*Recommended hardware: an OpenGL compatible graphics adaptor.
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Terminology and Acronyms
Analysis Entry – A single entry comprised of several Scan Entries which contains information
required for an analysis between scans and/or their analysis results.
Polar-Map (PM) – A 2D rendering of the left ventricle myocardium that enables complete
visualization without occlusions.
Scan Entry – A single entry that includes a scan and all of the data required to process that scan.
Study – A list of Analysis Entries that are saved together with accompanying data for future
processing and analysis.
FOV – Field of View: the spatial region that is sampled by the image.
GUI – Graphical User Interface
HLA – Horizontal Long-Axis
KM – Kinetic Model
LV – Left Ventricle Myocardium
SA – Short Axis
TAC – Time Activity Curve
VLA – Vertical Long-Axis
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FlowQuant© Graphical User Interface
The FlowQuant© GUI (shown below) is the main interface by which users interact with the program.
This GUI provides the means to setup a study list, process the study, and view its results.
Study Name
Menu
Unsaved study indicator
Entry re-ordering
buttons
Toolbar
Custom settings indicator
Species Icon
Settings unlocked
Scan Entry
Analysis Entry
Tracer (red signifies a difference
from the filename)
Study List
scrollbar
Process Buttons
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Menu
The menu system contains all functionality pertaining to study files, settings, as well as various
analysis tools. The menu includes the following hierarchy and shortcut key combinations in
parentheses:
File
o
Load Study (CTRL-O)
o
Save Study (CTRL-S)
o
Save Study As (CTRL-A)
o
Clear Study
o
Add Analysis Entry (CTRL-N)
o
Add Scan Entry (CTRL-E)
o
View Study Directory
o
Exit (CTRL-X)
Settings
o
Edit Study Settings (CTRL-P)
o
Save Current Study Settings as Default
o
Load My Default Study Settings
o
Save Study Settings
o
Load Study Settings
o
Load Factory Settings
Tools
o
Close all figures (CTRL-F)
o
Clean Study Directory
o
Update Scan File Directories
o
Image Cropper
o
DICOM Conversion Server
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Administrator Tools
Data
o
Export Dynamic Data
o
Export KM Results
o
Export ROI coordinates
Help
o
Help
o
Check for Updates
o
About
Toolbar
The toolbar contains quick access to a subset of functionality from the menu that is most commonly
used.
New Study
Load Study
Save Study
Add Analysis Entry
Add Scan Entry
Remove Entry
Duplicate Entry
Settings
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Study List
A list of analysis entries that may be batch processed in sequential order. This list forms the heart of
FlowQuant©, and may be considered as a list of analyses that the user requests. The entries and
their fields have context menus that may be accessed using the right mouse button. These context
menus provide additional functionality that is specific to the entry. The context menus vary with the
entry and field that is selected, therefore refer to the information below for more specific options.
Comments
This field allows the user to type texts associated to the study, which will be saved with the study
and reappear each time that it is opened.
Buttons
Several buttons exist on the GUI, including:
Study selection radio-buttons – selects which type of scan data location to add
-
Local Files – select individual image files stored locally
-
Local Directory – select an image directory stored locally (e.g. DICOM directory)
-
DICOM Node Q/R – perform a DICOM Query and Retrieve from a preconfigured DICOM
node.
Add Analysis – adds a new analysis entry to the study list.
Add Scan Entry – adds a new scan entry to the current analysis entry.
Up arrow – move the current entry (analysis entry or scan entry, highlighted in green) up in
the study list.
Down arrow – move the current entry (analysis entry or scan entry, highlighted in green)
down in the study list.
Process Buttons – process the study list in order from top to bottom. Four button
combinations exist.
o
Complete Files - All – process all of the study list steps that have not yet been
processed. Existing files are used if they are valid, otherwise they are overwritten.
This is useful for quick completion of only the missing data.
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o
Complete Files - Selection – process the entries that are selected by the checkbox.
Existing files are used if they are valid, otherwise they are overwritten.
o
Overwrite Files - All – process the entire study list without regard for existing files.
Existing files will be overwritten resulting in a longer processing time.
o
Overwrite Files - Selection – process the entries that are selected by the checkbox
without regard for existing files. Existing files will be overwritten resulting in a
longer processing time.
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Routine Use
Creating a Study
A study is created when it is first saved and it must be created for processing to take place. This is
due to the need to save result files during processing. The study file (named with a *.std extension)
can be saved to any directory, but by default will be saved to the C:\FlowQuant\Studies directory
(see Administrator Tools for more detail). When the file is saved, a subdirectory with the same name
will be saved in the same directory.
The study file contains all of the data required by FlowQuant©, and the directory contains all of the
result files.
Several menu options (and toolbar buttons) relate to the study:
-
New Study– clears the existing study from FlowQuant©.
-
Load Study – loads a previously saved study file into FlowQuant©.
-
Save Study– saves the current study. If the study has not yet been saved, the user is
queried for a study name and a directory in which to save it.
-
Save Study As – saves the current study under a new name and/or directory without
removing the original study and corresponding results files.
If a new study has been created and processed before saving, the user is first queried for a study
name and directory in which it will be saved.
Tip Use descriptive file names and organized directory structuring that will enable you to
locate a study even in the distant future.
Tip If a single patient is being processed, for example for a clinical case, consider saving the
study in the directory with the original patient data.
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Adding an Analysis Entry
An analysis entry may be added either through the menu or the button on the GUI. When this
option is selected, a new dialogue window opens enabling the selection of a single scan or multiple
scans to be added from an accessible directory. A new analysis entry is added at the bottom of the
study list. In the Analysis field the user may choose an analysis type from the pull-down menu.
This analysis entry contains 2 scan entries
FlowQuant automatically determines the type of analysis based on the type of scans that were
selected:
Rest-Stress Analysis – if one rest and one stress scan were selected. For this particular study
type, a special dialogue is displayed to enter heart rate and blood pressure data.
Mismatch – Normalized whole LV analysis – if one metabolic (FDG or acetate) and one
perfusion (Rb or ammonia) scans were selected.
Each analysis entry has analysis settings that may be edited by the user. By default these settings
are left blank, reverting to the study settings as described in the Settings Hierarchy section on page
23. The analysis entry settings may be accessed by right-clicking on the desired analysis entry and
selecting Process Analysis Settings. If the settings are not all empty (i.e. if the user has entered
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values that are different from the default study settings) a red exclamation mark will appear to the
left of the analysis entry once the OK button has been selected and the “Analysis Settings” menu
closes.
Adding a Scan Entry
Using either the button on the GUI or the menu, the user may add a scan entry into the currently
selected analysis (highlighted in green). The user will be queried for an image file. Once the file is
selected, the scan analysis entry fields will be automatically populated based on the file header
which must have been saved to the same directory as the image file. Ensure that the right tracer
and state have been determined.
The scan entry fields are as follows:
-
Patient – a unique name for the individual. By default this will be the patient name. If
the mouse cursor is placed over the field, a tool tip with the species is displayed for user
confirmation. The species is also indicated by the icon to the right of the patient entry
field. This can be changed by right-clicking on the icon and selecting a different species.
-
File – the location of the file containing the image data.
-
Image Type – indicates whether the scan is dynamic (D), gated (G), or static (S). This is
automatically determined by the image header and can be changed by the user by
selecting a different image type.
-
Tracer – the radio-tracer used for imaging (automatically determined from the image
header).
-
State – the patient’s (rest or stress) state during acquisition of the image (automatically
determined from the image header).
-
Label – a description of the image. The list of available labels is determined from the list
in the global options and is filtered by the tracer.
-
Orientation – the study label based on which the LV polar-map should be sampled. If
the orientation is the same as the study-tracer-label combination of the same scan, the
LV polar-map will be obtained from the same image; otherwise, the polar-map data of
another image will be used to sample the polar-map. The required orientation file is
expected to already exist; therefore, the options available in the pull-down relate to the
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scan entries above. There are three possible ways for this sampling from a previously
processed image to proceed as indicated by the lock button that appears to the right of
the orientation drop-down menu:
: use orientation to guide sampling
: lock sampling points
: lock only ellipse size
To toggle between the modes simply click on the icon.
-
Kinetic Model – the kinetic model that will be used to process the image. If Default
Option is selected the model is chosen based on the tracer and the species of the
subject. If “None” is chosen, kinetic modeling will not proceed.
Each scan entry has settings that may be edited by the user. By default these settings are left blank,
reverting to the study settings as described in the Settings Hierarchy on page 23. The scan entry
settings (described in Scan Entries, page 23) may be accessed by right-clicking on the scan entry and
selecting Process Scan Settings. If the settings are not all empty (i.e. if the user has entered values
that are different from the default study settings) a red exclamation mark will appear on the scan
entry once the OK button has been selected and the “Scan Settings” menu closes.
Likewise the Subject Exam Data including heart rate, blood pressures, glucose levels and tracer
specific activity can be edited. The Table below lists how these parameters are used.
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Parameter
Units
Usage
Heart Rate
bpm
Rate-pressure product correction of rest flow values
Coronary vascular resistance (CVR) in stress
perfusion scans
Systolic Blood Pressure
mmHg
Rate-pressure product correction of rest flow values
Diastolic Blood Pressure
mmHg
Rate-pressure product correction of rest flow values
Glucose Values
Mmol/L
Measured glucose values used for calculating the
MGU values from the Patlak model for FDG scans.
Once entered, the values will be averaged resulting
in a single value.
Specific Activity
GBq/μmol
Tracer Concentration (nmol/cc) uptake values
Tracer Activity
-
Patient Weight
Standard uptake values (SUV) calculations
Kg
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- Patient Height
- Activity before injection
- Residual activity
- Assay time before injection
- Residual assay time
CTAC image file
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Meters
MBq
MBq
hr:min:sec
hr:min:sec
Filename
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CT and emission data fusion in Dynamic Splash
Display
Processing a Study
By clicking on one of the process buttons, batch processing of the selection is started from top to
bottom of the study list. First, all of the scans of an analysis entry are processed, and then the
analysis entry is processed.
The scan entry processing consists of several steps that follow in sequence:
Reorientation
An uptake image is generated by summing the uptake frames, as specified in the uptake field of the
scan entry. Three orthogonal slices are taken in which the LV is registered. The slices are processed
sequentially, starting with a transverse plane. The reorientation tool allows the user to monitor the
process as well as manually intervene, if required. The transverse plane may be modified by sliding
the arrow (shown in green) on the grey slide bar to the left of the Transaxial Plane figure. Similarly,
the gut cropping slice (which allows gut/liver activity to be cropped from the FOV) can be
manipulated using the gut bar (blue) on the same slide bar. The plane and gut settings can be preset
in the scan settings dialogue or left blank, in which case they will be automatically determined at the
start of processing each scan. Additionally, the colour saturation of the image may be modified for
better visualization of the myocardium by sliding the green arrow shown on the Colour Saturation
slider bar.
The process begins with completely automated fitting; a countdown timer (shown in parentheses on
the accept button) provides the time for the user to intervene. Once any change is made, the timer
stops and the user is no longer limited by time. If no changes are made and the time runs out, the
results are accepted and the LV model fitting (LV sampling) stage is initiated. The user may also click
the accept button if no intervention is required. The user intervention time may be set in the
General Options dialogue of the study settings menu.
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In each of the three orthogonal planes, a partial ellipse is fit to the LV (shown in red). The user may
change the location, angle, and size by moving the lines, points, and ellipse respectively.
In the event that the orientation is determined based on that of another scan, the size and/or angle
may be locked (see Adding a Scan Entry on page 15). If, however, the user insists on changing the
size and angle, the lock at the bottom center of the window may be clicked. Clicking the lock swaps
between locked (red) and unlocked (green) states.
The Reorientation Tool contains additional information such as the orientation source (in the
transaxial plane figure) and whether the position, angle, and size of the ellipse in each slice was
automatically determined, manually determined, or fixed. The signal-to-noise ratio (SNR) and
myocardium-to-blood ratio (MBR) are displayed in the mid-VLA and mid-HLA frames, and file
information is displayed in the basal-SA frame.
The intention of this tool is to minimize user bias. Therefore, intervention should be at the early
stages, such as selecting the plane and gut. The user should look for good overlap of the synthetic
ellipse diagrams with the LV in the image. In addition, the last (bottom right) image is of a short axis
slice through the base of the LV and should have a centered circular pattern. The tool does not need
to result in a perfect fit since final registration and sampling of the LV occurs in the next step.
LV Modeling (Sampling)
The LV modeling stage detects the exact location of the center of the myocardium. The reoriented
image is re-sliced in a bottle-brush fashion to generate a sequence of slice images with a circular
pattern. A spline model with 13 degrees of freedom is then fit to the image. The Short Axis
Rotational Control, an additional sampling point/line exterior to the septal wall, is present on a
single slice image. This line indicates the center of the septal wall and is included to ensure that the
septum is displayed in the common orientation on the polar-map (i.e. centered on the left side of
the polar-map). Manual adjustment varies the short axis angle from 0°, as shown in the bottom right
corner of the window. The figure on the following page demonstrates the slices from apex to atrium
(top left to bottom right). Similarly, the horizontal and vertical long axis slices are displayed.
The fitted model is displayed as a red line (except in the horizontal long axis, where it is cyan). In the
short-axis slices the epicardium and endocardium are also drawn in solid red lines.
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Transverse
plane slider
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Fitted Ellipse
Parameter
optimization status
Gut crop slider
Orientation source
Accept button with
countdown timer
Angle control
Position control
Size control
Color saturation
slider
Fixed settings
lock/unlock
A countdown timer as in the Reorientation Tool exists, providing time for the user to intervene if
need be. The user may drag any of the rings in the short-axis slices of VLA/HLA to manually assist
with the fit. Each ring in the short-axis slices is paired with a ring in the VLA (red) of the HLA (cyan).
Also, if the septal wall sampling point/line does not appear to be centered on the septal wall, the
user may change its orientation by dragging the point/line. The green circle, which is fit to the apex
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in the VLA and HLA frames, may also be manually adjusted. The user may also click the Optimize Fit
button to improve the fit using the manual fit as a starting point. The Common image scale checkbox allows the user to swap between independent scaling of each image in the figure (for improved
contrast) and a common scale for all slices.
Short Axis Rotation
Control
Manual
intervention spline
points
Accept button with
countdown
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Once the LV model has been displayed, the Registered Polar-map, a static uptake polar-map and
model figure, is also shown for visualization of the whole LV to ensure proper fitting. The model
figure is displayed from three different angles to overcome visual occlusion. Missing sectors (sectors
that are outside the FOV) are not displayed. Once the LV model has been accepted, a larger version
of this figure is displayed.
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A drop-down menu appears in the Registered Polar-map window which gives the option of viewing
the 3D polar-maps as a 3D Surface (default), Smoothed 3D Surface, or 3D Mesh.
Dynamic Polar-Map
The orientation and sampling are then applied to all time frames of the image sequence. This
generates a dynamic polar-map as well as blood time activity curves. Three blood time-activitycurves are sampled: left ventricle cavity, left ventricle base, and left atrium.
A TAC figure is created with the three blood TACs, their median, and their mean myocardial (polarmap as shown on the PM) TAC.
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A gamma-variate model is also fit to the Blood Media TAC and the model parameters are displayed
in red for reference.
During this stage, motion detection takes place. If motion correction is turned on correction is also
applied. The small shift graph represents motion in x (septal-lateral), y (anterior-posterior), and z
(apex-base) direction in mm. The vertical black line on both the motion and TAC curves represents
the cutoff frame for which motion detection was applied (right of the line).
Blood ROI Processing
This processing step happens in the background. A blood pool frame is automatically selected based
on the blood TACs and the image is used to automatically define a blood ROI which may be used as
a blood input function to the kinetic model stage in place of the previously discussed regions (ABC).
The LV model figure is also updated with the blood ROI shown as a red patch.
Kinetic Modeling
The last stage of processing a scan includes running of the kinetic model. Description of all kinetic
models is beyond the scope of this document, but they all result in a similar figure format. A series
of polar-maps are displayed for the uptake, kinetic model free variables, chi-square, r-square, exit
flag, and upper bound saturation. At the bottom half, fitting information for the selected sector is
displayed. By default the mean of the high uptake regions is displayed, but the user can click on any
sector of the polar-map to view its specific fitting data.
The fitting graph shows the following activity curves:
Blue points: measured myocardial activity
Solid blue line: the model fit to the measured myocardial activity
Cyan line: pure myocardial signal
Solid red line: measured blood activity
Dashed red line: metabolite-corrected blood activity
Dashed green line: the difference between the measured myocardial activity and the fit at
that point (blue points less the blue solid line), i.e. the residuals
In cases where myocardium to blood pool region spillover correction is used, the sampled blood TAC
is shown with a shaded red line and the spillover corrected blood TAC (which is used for the kinetic
modeling input function) is shown in red.
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Tip Recycling windows may be important to reduce the chance of exhausting computer
resources. This can be selected in “Study Settings”.
Tip To abort processing, close the current window during processing.
Tip To process a single entry (analysis or scan entry), right-click on the entry and select
Process Scan (Overwrite or Complete) from the context menu.
Single Window Processing
Optionally, the user can choose to process a dynamic study using a single window, rather than all
the figures shown above. The same processing steps apply, with similar operator interaction. No
approval is required between steps, however, and processing continues from point of interaction.
This option may be turned using the study setting explained below.
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Analysis
Upon completion of the scan entry processing, the analysis selected in the Analysis drop-down list
will proceed. There are four main types of analysis available:
Rest-Stress
Mismatch
Database Comparison (*not yet fully activated)
Gated Animation
Rest-Stress
This analysis method provides rest, stress, reserve (stress/rest), difference (stress-rest) and
stress/rest>threshold (where threshold is the value set by the user in the Study Settings menu;
values < threshold are considered to be defects) polar maps for each of the relevant parameters
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from the kinetic model processing. For example, for the 1-compartment DV model, polar maps for
uptake DV, K1 and flow are presented. Below each polar-map, the mean and % of maximum are
given for each major coronary territory, and the segment with the lowest mean also indicated. For
an example of the output please see the Flow Defect Quantification figure on the subsequent page.
The polar-map is segmented based on the segment model set in the Study Settings menu. The
parameter values in each segment are saved in a text file. For an explanation of the output values
generated in the text file that accompanies the visual output please consult the Rest-Stress Defect
Analysis Output File Guide as listed in the Additional Documentation section at the end of this
manual.
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Mismatch
This analysis method provides a comparison between the uptake of the perfusion tracer and a
viability tracer, for example N-13-ammonia and FDG. Polar maps of:
-
uptake
-
defect area (area < threshold) normalized to the maximum value of the LV
-
match (perfusion defect – mismatch)
-
mismatch (FDG – perfusion)
-
reverse mismatch raw (perfusion – FDG)
-
reverse mismatch normalized (perfusion – FDG normalized to maximum of LV)
are presented. Above each polar-map, the % of LV that corresponds to that parameter is indicated.
For an example of the output please see the Mismatch Analysis figure on the subsequent page.
The polar-map is segmented based on the segment model set in the Study Settings menu. The
parameter values in each segment are saved in a text file. For an explanation of the output values
generated in the text file that accompanies the visual output please consult the Mismatch Scores
Output File Guide as listed in the Additional Documentation section at the end of this manual.
Note that there are six different mismatch options:
-
Normalize whole LV: this is the standard option
-
LBBB exclude septal half-LV: to be used in cases of left bundle branch block where it is not
useful to include the septal half-LV in the analysis
-
LBBB exclude septal wall: to be used in cases of left bundle branch block where it is not
useful to include the septal wall in the analysis
-
LBBB lateral wall only: to be used in cases of left bundle branch block where it is only useful
to include the lateral wall in the analysis
-
DBM – no FDG normalization: to be used in cases of diabetes mellitus where FDG
normalization is not useful
-
Normalize whole LV using K1 map: use the K1 map for the perfusion tracer rather than the
uptake map.
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Database Comparison
Allows comparison of rest/stress scan pairs to a normal population database. Note that this feature
is not fully functional at this time.
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Gated Animation
Gated scans are processed in a similar fashion to dynamic scan, beginning with the Orientation and
PM Sampling stages detailed above. LV sampling is then automatically processed for each phase
separately. A gated report is generated for each scan as shown below. The report is gated and cycles
through the phases synchronously for all scans.
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During cine playback the user may change the frame rate (top right scroll); change the zoom on the
SA, VLA, and HLA (top left scroll); capture the sequence to a movie file (bottom left button), or
pause/resume the cine display (bottom right button). In addition, the user may click on the X marks
in the volume vs. phase curve to select a frame to pause the display on. Time frames are always
synchronized between all reports.
Results
Images of the results are saved as image files to the study directory; the file type can be selected in
the Study Settings menu. If the option is selected in the Study Settings, these results may also be
printed to the default printer.
Reports can be saved to an additional directory by checking “Enable spooling” in the Study Settings
dialogue.
Dynamic Splash Display (DSD)
Dynamic Splash Display is an interactive GUI that provides the user tools to visualize processed
studies. DSD is intended to interpret rest and stress perfusion studies, but is compatible with
dynamic, gated and static images, providing more advanced functionality. Studies can be of the
same or different patients or baseline vs. follow-up. DSD allows the user to also view CT images of
the same patient fused with emission images.
If dynamic images are present the user has the ability to play trough the image sequence and view
time activity curves. Screen captures can be saved as movie or still images. Movies can be saved in
*.gif or *.avi format while images are saved in JPEG format.
The header at the top of the figure contains relevant patient data (e.g. patient identifiers, patient
age, patient weight, blood pressure, heart rate). A series of buttons controlling majority of the
features are located at the bottom of the figure. The buttons control everything from the colormap
being displayed, to the zoom of the image.
By default, the DSD shows select slices through the LV and the toggles located above each image
can be used to scroll through the slices being displayed and to align between image series. Similarly
the frame slider toggle at the bottom of the figure allows the user to change which frame is
currently being displayed on the figure if the images are dynamic or gated. The Time Activity Curves
plotted in the DSD are also interactive. By moving the “blue bar” around the user can change the
time frame being displayed. If the user drags the bar to cover multiple time frames the images will
update to a summation of the time frames.
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The user also has the ability to view the contour lines on the image by toggling them on and off.
DSD also allows the user to fuse PET and CT images together for further comparison. Using the slider
located below the Time Activity Curves the user can select mixing of the CT and emission images. By
default 100% emission data will be displayed. If no CT data is loaded into FlowQuant this slider is not
visible.
A list of addition features in DSD is as follows:
Ability to change the color-limits of the image
o
Custom - Using a slider or preset values
o
Study - Max and min of the entire data set
o
Frame - Max and min of entire data set within a frame
Changing the colormap
o
Inverse of colormap
Changing the x and y scale of the TACs
o
Logarithmic or linear
Settings the Zoom of the Image
Changing the image slices being displayed
Changing the image frame being displayed (dynamic/gated only)
Image Transparency (CT data required)
Playback of images (dynamic/gated only)
o
Loop (forward)
o
Sweep (forward then backwards)
o
Changing speed of playback
Enabling contour lines
o
Display or hide
o
Change color
Saving (Screenshot or movie)
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Screen shot - JPEG

o
Slice Slider
Zoom Slider
35
Printer friendly version (White background)
Movie - GIF or Avi
Patient Information
header
Frame Slider
Playback Settings
TAC slider
Color Limit Toggles
PET-CT
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Additional Features
Many additional features may be accessed through context menus associated with an entry in the
study list (analysis or scan entry). Context menus appear on the screen when the user clicks on an
item using the right mouse button. The contents of the menus change depending on the object that
was clicked. Some entries in the menu are common to the entry (analysis or scan), and will
therefore appear regardless of which part of the entry was clicked. Other entries are specific to the
field.
The common context menu entries include:
Analysis Entry
Scan Entry
Subject Exam Data
Description
Physiologic data associated
with the exam (heart rate,
blood pressures, glucose
levels)
Process Analysis Settings
Process Scan Settings
Settings associated with the
entry.
Process Analysis (Overwrite)
Process Scan (Overwrite)
Process the entry,
overwriting existing results.
Process Scan (Complete)
Process the entry,
completing only the results
that have not yet been
processed.
Process Analysis (Complete)
Duplicate
Duplicate the entry.
Remove
Remove the entry from the
study list.
View Results
View results (a sub-menu lets
the user select the desired
result to view).
Delete Results
Delete results (a sub-menu
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lets the user select a set of
results to delete).
Export Results
Export the blood TAC to a
CSV (comma separated
variable) file.
Subject Exam Data
Enter heart rate, blood
pressure (systolic and
diastolic), and glucose values.
Specific context menu entries include:
Filename:
-
View – view the raw image.
-
View Smoothed – view the raw image after it has been smoothed to the resolution
specified through the settings hierarchy.
-
View Header – view the image header information.
-
Select File – select an image file using a browser.
-
Crop File – crop out parts of an image that are not relevant to the analysis and may
adversely affect software automation.
-
Motion-Correct File – adjust for patient motion.
Orientation:
-
Import Orientation – import the orientation from a previously processed file
(*PMSampling.mat file)
Removing an Entry
Select the entry > Press the delete button in the toolbar.
OR
> Right-click on the entry and select “Remove”.
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Confirm the removal by clicking on the “Yes” button in the confirmation pop-up box.
Duplicating an Entry
Select the entry > Click on the duplicate button in the toolbar.
OR
> Right-click on the entry and select “Duplicate” from the context menu.
The duplicated entry is entered at the bottom of the study list for an analysis entry, or at the bottom
of the analysis list for a duplicated scan entry.
Multiple Entry Selection
Hold the Control/Ctrl key > Click on the entry/entries of interest > Release key when done.
This function is useful for removing, duplicating, processing, and changing the settings of several
entries at once.
Note: Multiple entries do not currently support result viewing.
Note: Only entries of the same type (i.e. analysis or scan) can be selected simultaneously to avoid
ambiguity.
Viewing Data
In a scan or analysis context menu under “View Results”, several of the datasets may be viewed.
These include:
-
Header
-
Dynamic Image *
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Uptake Image *1
-
Smoothed Uptake Image
-
PM Sampling
-
PM Sampling Validation Tool
-
Reoriented Image
-
Smoothed Reoriented Image
-
Dynamic Image Splash
-
Uptake PM
-
Dynamic Sequence Viewer
-
Dynamic Sequence Report
-
KM Data (blood time-activity-curves and dynamic polar-maps)
-
KM Results
-
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39
Context menus also exist for 3D surface viewing of polar-maps. By right-clicking on any polar-map or
3D surface, a context menu with the following viewing options will appear:
*
-
View Polar-map
-
View 3D Mesh – view a 3D rendering of the polar-map with the surface mesh displayed.
-
View 3D Surface – view a 3D rendering of the polar-map with the surface mesh
displayed and a softer lighting which gives a smoother appearance.
-
View Smoothed 3D Surface – view a 3D rendering of the polar-map which has been
smoothed using the spline points.
-
Apply to all PMs in figure – apply current view to all other polar-maps.
-
Copy to separate figure – copy the current subplot and its view to a separate figure.
Volumetric data may be viewed with either VolumeViewer or 4DView. For further information, please refer
to their respective documentations (page 47).
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Analysis Settings
During the different processing stages, certain parameters are used which may be controlled by the
user through a hierarchy. When a new study is created, default study settings are loaded. When a
new scan or analysis entry is added, default entry settings are used. The user can modify the scan
entry settings, analysis entry settings, and global settings, which are saved as part of the study.
Settings Hierarchy
When processing a study, the actual settings for processing are resolved based on a hierarchy, as
demonstrated in the figure below.
Analysis Setting
Study Setting
o
Species + Tracer
Highest (most specific)
Priority
Scan Setting
Lowest (least specific)
o Species
Scan settings are specific for a scan entry and therefore are top priority. Settings that are common
o Default
to all scan entries
in an analysis entry may be set through the analysis entry settings. However, if
conflicting entries exist between analysis and scan entries, the scan setting will always prevail as
dictated by the hierarchy.
Study settings are split into combinations of species and tracer. Thus, the user can specify different
default settings for species-tracer combinations. The hierarchy dictates that settings that are
species-tracer specific have higher priority than settings of the species alone. At the lowest level of
the hierarchy are default settings that are not specific to any species or tracer.
If settings (global, analysis, and scan) are left empty, default values will take effect, which are
determined by working backwards through the hierarchy. Therefore, if a setting is not specified for a
scan, the analysis setting will be used. If that hasn’t been specified either, the study setting for that
species-tracer combination is used. If that is set to default, the species setting is used. Finally, if the
species setting is set to default, the software default setting is used. The entire global settings can
be edited using the global settings dialogues.
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Entry Settings
The following image demonstrates the “Scan Settings” (settings for a scan entry). Likewise, an
“Analysis Settings” dialogue exists for an analysis entry, which differs in the scope of influence as
dictated by the settings hierarchy explained in the section above. Entry settings may be accessed
through the context menu of the respective entry.
The species section in both the “Analysis Settings” and “Scan Settings” menus allows the user to
override the species that was imaged, and may be useful if the wrong species is identified by the
software. This field is located at the top of the “Analysis Settings” and “Scan Settings” dialogue
windows, and can also be found under the Default Analysis Options heading in the “Study Settings”
menu. The species may be seen on the reorientation reports as well as in the tooltip of the patient
name. The species can be changed using the species icon to the right of the “Patient” field.
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The other sections relate to generating polar-maps and the kinetic modeling. If the entries are left
blank, default values will be used from lower levels in the hierarchy. Default values (if relevant) are
displayed based on the notation explained in the Default Value Display Feature section in orange
under Default Analysis Options. The default values are determined by the hierarchy specific for the
species and tracer of the scan.
The editable fields include:
o
Species – the species of the patient that was imaged (Automatically
Determine/human/dog/rat/mouse/pig).
Polar-map Options
o
Plane – the transverse plane in the image to use in the first stage of orientation
(integer value between one and number of planes)
o
Gut – the last transverse plane in the image to use for the analysis in order to crop
out gut/liver activity (integer value between 1 and number of planes).
o
Radial Search (%) (100-200) – currently not used.
o
Radial sample endo (mm) – the distance from the center of the myocardium to the
endocardium. Used in conjunction with Radial sample epi. Average activity over
depth of myocardium.
o
Radial sample epi (mm) – the distance from the center of the myocardium to the
epicardium.
o
Dynamic smoothing:
o

Type – type of smoothing (Default/Gaussian/Uniform/Peak) to apply to
dynamic volume sequence prior to obtaining dynamic polar-map.

Kernel size –size of the kernel used in smoothing.
Uptake – the frames which are summed to generate an uptake image. The default is
1 (meaning the last frame). However, the user can enter integer numbers to
indicate the last N frames to sum. The user can also specify a range of frames from
anywhere in the sequence over which to sum.

o
Weighted Sum: Default/On/Off.
Uptake resolution (mm) – target smoothing resolution (0-20 mm) of uptake images.
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o
Normal uptake threshold (%) – the threshold in percent of maximum activity in the
polar-map above which sectors are regarded as normal.
o
Segment model – the segment model (3, 5, 9, 17, or 20) to apply to the polar-map
for analysis.
o
NRings – the number of polar-map rings to use with the segment model.
Kinetic Modeling Options:
o
Start time (mins) – number of minutes from the start of acquisition at which to start
the dynamic data for kinetic modeling.
o
End time (mins) – number of minutes from start of acquisition at which to end the
dynamic data for kinetic modeling.
o
Blood spillover correction – correct for blood to myocardium spillover.
o
Auto estimate RC – automatically determine the recovery coefficient to be used for
partial volume correction.
o
Recovery Coefficient– preset recovery coefficient if a constant RC model is used (01)
o
DV (K1/K2) – preset distribution volume value if a constant DV model is used.
o
Retention integral – means by which to obtain the retention integral for the
retention model. (Use default/Peak + constant time [0-2 min]/Time/Gamma fit)
o
Blood input – regions of the blood pool used to generate blood time activity curve
for kinetic modeling and retention model. Options include:

All combinations of atrium (A), base (B), and cavity (C)

ROI generated from an early blood pool image

External file
o
RV blood correction – optional correction for RV blood spillover into the
myocardium ROI.
o
Fast flag – choose either to process each sector of the polar-map or ¼ of sectors and
interpolate; used to speed up kinetic-modeling processing (Default/Yes/No).
Coronary Artery Tree:
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Locations of stenoses can be entered for the major arteries. The arteries will then
be displayed on the polar-maps and 3D views of the LV. Anatomy options include:
default, none, right dominant, left dominant.
Extra TAC File:
Select an external file containing a TAC to which TAC from the scan can be
compared. Supported formats are comma separated variables (*.csv) files from GE
micro volumetric blood sampler and Siemens IRW and Asipro software.
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Study Settings
The “Study Settings” dialogue is shown below. The study settings are split into General Options,
Study Options, and Default Analysis Options.
General Options
The general options pertain to the general functioning of FlowQuant© and include the following
options:
User Interaction Delay Time (sec) – a setting is available for both batch-processing and
processing of a single scan. The time is specified in seconds (enter 0 for no user intervention
and infinity (inf) for mandatory user confirmation).
Recycle analysis windows – if checked, windows are reused rather than created for each
new figure. This feature is especially useful when batch-processing.
Warning If this feature is not used, many windows may be opened, leading to poor system
respons.
Volumetric Viewer – selects which viewer the user prefers to use for viewing results
(Volume Viewer / 4D Viewer).
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Reports to Save – determines which reports to be saved, in which image format, and to
what locations. The following report types can be individually configured: Orientation
(includes reorientation, LV model, uptake polar-map, and TAC figures); Kinetic modeling;
Analyses. Each report can be saved to one or more of the following:
o
Save – Local file in the study directory
o
Print – Print to the default local printer
o
Spool – Send to another directory for spooling into an archiving system (only tested
with Hermes). Red text in the spooling directory text box indicates that the specified
directory cannot be found. Supported file types are *.png, *.tif, or *.gif.
o
DICOM – push as a secondary screen capture to a DICOM complaint PACS system
Supported image formats are:
o
File Formats – the file formats which the reports will be saved in include:

Matlab Figure (*.fig)

Post Script (*.eps)

Enhanced Metafile (*.emf)

Portable Network Graphics (*.png)

TIFF, Compressed Image (*.tif)

Print to default printer (Note: this option may be convenient in some cases,
but may also lead to excess waste of printer supplies).

Gated Report (*.mpeg)
Gated reports can only be saved as animated *.gif files to the local study directory.
This section includes options that are specific to the type of study and includes the following
options:
Scan Labels List – a list of possible labels that are available in the label pull-downs of each
scan entry. The list should be edited to reflect the nature of the study. They should typically
follow the format descriptionTracer where the description may include rest, stress, baseline,
follow-up, 240s infusion, etc. Below are some examples:
Example study
Example labels
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Comparison of perfusion with Rubidium and RestRubidium
Ammonia
StressRubidium
RestAmmonia
StressAmmonia
Clinical use with Rubidium and FDG mismatch RestRubidium
analysis
StressRubidium
RestFDG
StressFDG
The tracer section will be used to help resolve the relevant labels to each entry based on the
tracer in the image information.
Apply scatter fraction correction – enable/disable correction for scatter fraction if need be
(specific for Rb scans on GE scanners). *No longer required depending on the GE camera
model/software.
Save reoriented conical slices – turns on an optional saving of an additional intermediate
file with the reoriented uptake frames sampled in a spherical-conical coordinate system.
Copy images to study directory – copy the image files to the study directory. This feature is
useful for transferring an entire study to one directory; however, it increases disk usage.
Live PM display during LV modeling – displays the PM and three orthogonal views for
quality control during short axis sampling.
Process RV – enables segmenting and analysis of the RV myocardium in addition to the LV
myocardium.
Color Options
Color scheme – changes the colour scheme to white, grey, or black
Image Color-map – changes the color-map of the image to either: Jet, HSV, Hot, Cool,
Spring, Summer, Autumn, Winter, Gray, Bone, iBone, Copper, Pink, or HotMetal
Polar-map Color-map - changes the color-map of the polar-maps to either: Jet, HSV, Hot,
Cool, Spring, Summer, Autumn, Winter, Gray, Bone, iBone, Copper, Pink, or HotMetal
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Preferred Uptake Units - activity Bq/cc, SUV-bw mL/g, SUV-lbm mL/g, or SUV bmi mL/gm2. Note
that SUV values can only be displayed if relevant patient information (weight, height, sex) can be
retrieved from the scan file header. In the absence of relevant data, activity units are displayed.
Default Analysis Options
This section pertains to default values for analysis. Note that the fields in this section are similar to
those in the process scan/analysis settings dialogue. The description of each field in this panel is
explained in the “Entry Settings” section above.
The user may select combinations of species and tracer, and general default and default values for
different species using the two pull-down menus at the top of the panel. Default values, which are
determined through the hierarchy, are displayed using the notation as explained below:
Element
Default
User-Defined
Edit Boxes
Blue text
Black text
Pull-Down Menus
Shown in tooltip while
hovering cursor over
pull-down menu
Radio Buttons
Bold text
Regular text
Rest-Stress Flow Analysis Options
These options control processing and reporting of Rest-Stress Analyses. Options include:
Normal Rate-Pressure Product (RPP) – rate pressure product to which rest perfusion scans are
normalized for RPP correction.
Normalize only if RPP is greater – optionally applies normalization of flow to normal RPP if RPP is
greater than the normal RPP. Otherwise normalization will be applied regardless if RPP is greater
than or less than normal RPP.
Defect Clinical Classification
Method – determines the classification scheme by which flow segments are classifies
Gould – based on Nils P. Johnson, Lance Gould, "Integrating noninvasive absolute flow,
coronary flow reserve, and ischemic thresholds into a comprehensive map of physiological
severity", JACC, 2012:5(4);430-440.
Ottawa – unpublished
Prior – unpublished
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Apply RPP – controls if classification is performed using RPP corrected or uncorrected reserve
values.
Confidence intervals – optionally display confidence intervals around classification points. Intervals
can be specified for CFR and stress flow individually either as % of value or in absolute units.
Generate Summary Report – optionally generates a summary clinical flow reserve classification
report based on the either Flow or FlowRC values.
Making Current Study Settings the Default Settings
Select Menu > Settings > Save Current Study Settings as Default
This will set the default study settings for future studies.
Reverting to the Default Study Settings
Select Menu > Settings > Load My Default Study Settings
The user may load the default study settings to override the current study settings. The user is
prompted to confirm the operation, as the current settings will be lost.
Exporting the Study Settings
Select Menu > Settings > Save Study Settings
The user may export the current study settings to a file. The user is prompted for a file name and
location. The *.ini file is saved and may be imported in the future.
Note: The MMSettings.ini file in the FlowQuant© directory is the default study settings file. Saving
to this file is equivalent to “Making Current Study Settings the Default Settings” as explained
above.
Importing Study Settings from another File
Select Menu > Settings > Load Study Settings
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The user may import study settings from either an *.ini file, or from another study. This operation
overwrites the current study settings.
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Tools
Close All Figures
Closes all the FlowQuant© generated figures in order to de-clutter the screen.
Clean Study Directory
Removes all files from the study directory which are not relevant to the current study settings.
Update Scan Files Directories
This tool is designed to quickly correct the location of multiple image files, particularly in large
studies, which is particularly useful when the directory structure has been reorganized, or the study
has been copied to another computer. When the tool is opened all the existing file locations are
listed in the top. Select a file location that needs to be corrected and update the location it in the
edit box below. You may use the browse button to locate the new directory using a directory
browser. Finally, press the Apply to update the location in the current list of directories. The
directory locations are updated in the study when the OK button is pressed. Pressing the Cancel
button maintains the current locations in the study.
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Image Cropping Tool
The Image Cropping Tool is intended to crop out parts of an image that are not relevant (ex. a urine
pool under the animal, uptake in an adjacent organ, or irrelevant areas) to the analysis and may
adversely affect the software automation (ex. out-of-memory errors). The Image Cropping Tool may
either be accessed through the tools menu or by the context menu of a specific image filename
entry. If the Image Cropping Tool is accessed through the context menu the image filename will
already appear as the source filename, which will not be editable. If the tool is accessed through the
menu, the source file field will not be populated and the user will have to enter a file. Below is an
example dialogue accessed from the context menu.
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The cropped field can be selected in one of four ways:
1) Entering the 6 cropping coordinates directly on the left under Crop.
The inputs include the starting and ending X, Y, and Z slices to include in the cropped image.
By default the original image dimensions are populated.
2) Choosing a preset crop under Presets.
The presets crop the image so that half of the X and half of the Y dimensions and all Z planes
are kept. The buttons correspond to all combinations of left half (L); centre half (C); or right
half (R), and top half (T); middle half (M); or bottom half (B). When any of these buttons are
pressed, the X, Y, and Z edit boxes will update to reflect the new cropping coordinates.
3) Using Quick Pick.
Select the desired region by selecting the uptake frame (top scroll bar) and the transverse
slice (left scroll bar), and clicking on the centre of the LV.
Tip The uptake frame in which the LV is most clearly defined depends upon the specific
tracer. The Image Cropper Tool automatically selects the final frame; however, to
facilitate cropping choose the frame with the highest uptake before selecting the
transverse slice.
4) Using the Volume Viewer tool.*2
A range of frames to view may be specified in the edit box. By default, only the last time
frame is selected. If the images are large, selecting too many frames may lead to out of
memory errors. Once the desired time frame range has been selected, click the Use Volume
Viewer button.
The Volume Viewer enables the specification of cropping ranges by the moveable green and
red bars on the axis rulers. Accept results by clicking on the Acquire Volume button. The
* A link to the Volume Viewer documentation is found on page 42.
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selected cropping coordinates will be displayed in the coordinate edit boxes, mentioned in
option 1.
By default, the target file will have the same name as the source file with _cropped appended to
the end of the filename. The file will also be saved as a .mat file.
Click the save button to save the cropped image. If the Image Cropping Tool was accessed
through a context menu, the file entry will be populated with the cropped image file name.
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Motion Correction Tool
Tip As of version 2.2.0, automatic motion correction can be applied to dynamic images. The
motion correction tool described below is a manual correction.
The motion correction tool is used to determine if the subject moved during a dynamic scan. The
tool is accessed through the context menu of the image file and brings up the 4D viewer as well as
the motion estimation tool, which work in conjunction with each other.
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The user selects orthogonal x, y, and z planes on which the analysis is performed by moving the
crosshairs to the slices of choice in the 4D Viewer window. The motion correction tool is updated
with every pixel selected in the viewer. The correction tool shows cross correlations between
adjacent time frames in all three axes (top row) as well as on a zoomed scale (bottom row). In the
absence of patient motion, the darkest red regions would align on the zero-shift line. The tools can
be used together as follows:
1. Select the pixel as well as time frame in the 4D Viewer window.
2. Control points (marked by “+” symbols) are superimposed on the zoomed views. The user
can interact with the control points to correct motion by clicking and dragging each point. If
there is no motion in the image, best cross correlations (red) will run as centered, vertical
lines in all three axes. In practice some small deviations may be expected. The control points
should superimpose the cross correlations closest to unity (red). Select the highest
correlation (dark red) with the control points. This can be done in two ways:
3.
i.
Manually adjusting each control point by clicking and dragging them to the darkest
red regions for the X, Y and/or Z axes. Select the axes to optimize along by checking
“Enable X”, “Enable Y” and/or “Enable Z” below each zoomed frame in the Motion
Estimator window.
ii.
Using the Automatically Optimize button. Select the time frame to optimize by
clicking and dragging the horizontal black line to the desired time frame. The
optimization will apply to all frames below this line. Select the axes to optimize
along by checking “Enable X”, “Enable Y” and/or “Enable Z” below each zoomed
frame in the Motion Estimator window. Click Automatically Optimize.
Click Apply and the Motion Estimator and 4D Viewer windows will automatically update the
image.
Tip The playback feature in the 4D Viewer may be used in conjunction with the motion
estimation tool to evaluate image motion.
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4. When satisfied with the correction, press the “Save” button to save the image to a new file.
The new filename will automatically replace the existing one in the scan entry. The motion
correction can be cancelled by closing both windows.
Administrator Tools
The administrator tool provides additional advanced options that are intended only for a user
overseeing the FlowQuant installation. The administrator tool is password protected with the
default password set to “password”, but the user may choose to change the password after
receiving administrator access. The administrator tool can be used to configure default directories
for study and scan file locations, and tracer and state dictionaries can be edited.
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Dictionaries are used to configure synonyms that will be translated into standard terms used
throughout FlowQuant. The list of terms is displayed in the left half of the dictionary and the
synonyms of that terms are listed on the right. When looking to resolve a state, any synonym that is
encountered is translated into the corresponding term (same process for tracers). In the examples
below, the terms Water, OWater and H2O will be translated into Water. The patterns SStress,
Adeno, ATP of Stress will be translated into Stress. Patterns are sought in applicable image file
header fields and are delimited by characters (,\.^- spaces and by numbers).
Data – Export Dynamic Data
Dynamic data can be exported to an Excel spreadsheet for further analysis. Each entry that has been
processed (reoriented and sampled) is included in its own sheet. The sheet contains a table about
each time frame (rows).
Data – Export KM Results
This tool is useful for further analysis of the kinetic modeling results, by exporting the desired data
into an Excel spreadsheet. The user is queried where to save the results and is then queried for the
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desired parameters to record and into how many segments the polar-map should be divided. The
user may specify how many rings of the polar-map to use or let FlowQuant automatically determine.
An operation to perform on all pixels in a segment is also required (e.g. Mean, Median, StandardDeviation, Standard-Error, Maximum, Minimum).
A new sheet will be created with the results tabulated with each parameter, of each segment in a
column and each scan in a row. Only the available results (images that have been processed) are
tabulated. Parameters that are not part of an entry’s kinetic model are left empty. The order of the
entries is as specified in the study list.
Data – Export ROI Coordinates
This tool exports the ROI coordinates from the SA sampling phase of the processing to a CSV file.
This is useful for importing the desired region of interest into other software packages for further or
comparative analysis using the same initial registration of the data.
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Special Considerations for Small Animal PET Image
Processing
The previous sections pertained to image processing for scans in humans. The process is the same in
small animals; however, special considerations must be made to accommodate their smaller size.
Select SettingsEdit Study Settings
The default options for each species can be viewed by selecting the species from the “Species”
menu under “Default Analysis Options”. Settings specific to the species and tracer can be obtained
by additionally selecting the tracer from the “Tracer” menu. Species-specific settings are shown in
black text, whereas settings common to all species are shown in purple text. Although these settings
are designed for the specific species, they can be adjusted by the user by simply typing in the
desired value.
Image Cropping
ToolsImage Cropping Tool
OR
Right click the “File” field of the scan  Crop File
Due to the size of the image files in small animal PET, a memory error may result if the user
attempts to process the files without using the Image Cropping Tool first. General instructions for
using this tool are available in the Image Cropping Tools section.
Gut Cropping
During the use of the Reorientation Tool, the ellipse is automatically fit to the LV. Activity from the
liver/kidneys is prevalent in small animal PET images and this may interfere with the automatic
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ellipse fitting, polar-map, and kinetic modeling. The Gut Crop slide bar is automatically set at the
maximum number of planes (no cropping) and can be adjusted to any point along the transverse
plane. Once set it will crop out the image below the plane it has been set to. Shown below is
reorientation with (right) and without (left) gut cropping.
The gut contains a region of high activity, thus the ellipse is erroneously matched to this area (L). The Gut
Crop slider can be used to crop the gut to fit the ellipse to the LV more correctly (R).
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Additional Documentation
Rest-Stress Defect Analysis Output File Guide – guide to the text file output for Rest-Stress analysis.
http://www.lightbox.ca/~mfi/FlowQuant/Documentation/RestStress%20Defect%20Analysis%20Output%20File%20Guide.pdf
Mismatch Scores Output File Guide– guide to the text file output for Mismatch analysis.
http://www.lightbox.ca/~mfi/FlowQuant/Documentation/Mismatch%20Scores%20Output%20File%
20Guide.pdf
Volume Viewer User Manual – instructions on using the Volume Viewer tool.
http://www.lightbox.ca/~mfi/FlowQuant/Documentation/volViewer%20Manual.pdf
DICOM Convert Server User Manual – instructions on installing and configuring the DICOM Convert
Server.
http://www.lightbox.ca/~mfi/FlowQuant/Documentation/DICOM%20Convert%20Server%20User%2
0Manual.pdf
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